Many cell types can be identified and categorized by the abundance of specific sets of proteins endogenously expressed and located on their plasma membranes. This phenomenon enables the study of cells using a process known as immunophenotyping, in which cells are incubated with and bound by fluorescently-labeled antibodies that are specific to known surface proteins of the cells. Flow cytometry is commonly used to measure the levels of the surface-bound antibodies for each cell. However, flow cytometry-based approaches are limited by the number of fluorophores that can be used concurrently in the same experiment. Further, the number of fluorophores that can be used concurrently in the same experiment using flow cytometry-based approaches is limited by spectral overlap. Additionally, flow cytometry is not amenable to many biologically-relevant assays and subsequent DNA sequencing.